Proteomics is a rapidly expanding field but current methodologies remain inadequate for achieving its full potential. The most basic enzymological tool for characterizing proteins is the protease. Proteases are already an essential part of proteomic analysis but more sophisticated tools are needed to identify low abundance proteins in highly complex samples. We have engineered prototype "restriction" proteases which are active in denaturing conditions and which cut specifically at well-defined cognate sequence motifs. Our basic innovation would be the ability to parse a proteome into sequence-edited slices and to detect these edited portions with high resolution and high sensitivity. In Phase I we tested the prototype restriction protease for suitability in proteomic analysis and implemented a novel directed evolution methodology for the selection of proteases that cut new sequence motifs. The Phase II objective is to develop a sophisticated set of protease tools to facilitate proteomic analysis in the way restriction endonucleases have facilitated genomic analysis. PUBLIC HEALTH RELEVANCE: The complex and dynamic nature of proteomes make them rich with useful information but difficult to characterize. Our long-range objective is to develop a sophisticated set of protease tools to facilitate proteomic analysis in the way restriction endonucleases have facilitated genomic analysis. Better proteomic tools will lead to earlier detection of disease states, better treatments, better predictability of the effects of various treatments, and the development of individualized therapies.